Use of near-isogenic lines to precisely map and validate a major QTL for grain weight on chromosome 4AL in bread wheat (Triticum aestivum L.).
This study precisely mapped and validated a major quantitative trait locus (QTL) on chromosome 4AL for thousand-grain weight in wheat using multiple near-isogenic lines. Thousand-grain weight (TGW) is an essential yield component. Following the previous identification of a major QTL for TGW within the interval of 15.7 cM (92.7-108.4 cM) on chromosome 4AL using the Nongda3338 (ND3338)/Jingdong6 (JD6) doubled haploid population, the aim of this study was to perform more precise mapping and validate the genetic effect of the QTL. Multiple near-isogenic lines (NILs) were developed using ND3338 as the recurrent parent...
Source: TAG. Theoretical and Applied Genetics - May 22, 2019 Category: Genetics & Stem Cells Authors: Guan P, Di N, Mu Q, Shen X, Wang Y, Wang X, Yu K, Song W, Chen Y, Xin M, Hu Z, Guo W, Yao Y, Ni Z, Sun Q, Peng H Tags: Theor Appl Genet Source Type: research

Temporal genetic patterns of root growth in Brassica napus L. revealed by a low-cost, high-efficiency hydroponic system.
Abstract KEY MESSAGE: Application of a low-cost and high-efficiency hydroponic system in a rapeseed population verified two types of genetic factors ("persistent" and "stage-specific") that control root development. The root system is a vital plant component for nutrient and water acquisition and is targeted to enhance plant productivity. Genetic dissection of the root system generally focuses on a single stage, but roots grow continuously during plant development. To reveal the temporal genetic patterns of root development, we measured nine root-related traits in a rapeseed recombinant inbred ...
Source: TAG. Theoretical and Applied Genetics - May 17, 2019 Category: Genetics & Stem Cells Authors: Wang J, Kuang L, Wang X, Liu G, Dun X, Wang H Tags: Theor Appl Genet Source Type: research

Extensive changes in gene expression and alternative splicing due to homoeologous exchange in rice segmental allopolyploids.
We report rampant homoeologous exchanges in progenies of a newly synthesized rice segmental allotetraploid and demonstrate their consequences to changes of gene expression and alternative splicing. Allopolyploidization is recurrent across the tree of angiosperms and known as a driving evolutionary force in both plants and animals. A salient feature of allopolyploidization is the induction of homoeologous exchange (HE) events between the constituent subgenomes, which may in turn cause changes in gene expression, transcript alternative splicing, and phenotypic novelty. However, this issue has been poorly studied, largely bec...
Source: TAG. Theoretical and Applied Genetics - May 16, 2019 Category: Genetics & Stem Cells Authors: Zhang Z, Fu T, Liu Z, Wang X, Xun H, Li G, Ding B, Dong Y, Lin X, Sanguinet KA, Liu B, Wu Y, Gong L Tags: Theor Appl Genet Source Type: research

Genetic architecture of maize chlorotic mottle virus and maize lethal necrosis through GWAS, linkage analysis and genomic prediction in tropical maize germplasm.
The objective of the present study was to gain insights and validate the genetic architecture of resistance to MCMV and MLN in maize. We applied linkage mapping to three doubled-haploid populations and a genome-wide association study (GWAS) on 380 diverse maize lines. For all the populations, phenotypic variation for MCMV and MLN was significant, and heritability was moderate to high. Linkage mapping revealed 13 quantitative trait loci (QTLs) for MCMV resistance and 12 QTLs conferring MLN resistance. One major-effect QTL, qMCMV3-108/qMLN3-108, was consistent across populations for both MCMV and MLN resistance. Joint linkag...
Source: TAG. Theoretical and Applied Genetics - May 16, 2019 Category: Genetics & Stem Cells Authors: Sitonik C, Suresh LM, Beyene Y, Olsen MS, Makumbi D, Oliver K, Das B, Bright JM, Mugo S, Crossa J, Tarekegne A, Prasanna BM, Gowda M Tags: Theor Appl Genet Source Type: research

GNI-A1 mediates trade-off between grain number and grain weight in tetraploid wheat.
Abstract KEY MESSAGE: Wild emmer allele of GNI-A1 ease competition among developing grains through the suppression of floret fertility and increase grain weight in tetraploid wheat. Grain yield is a highly polygenic trait determined by the number of grains per unit area, as well as by grain weight. In wheat, grain number and grain weight are usually negatively correlated. Yet, the genetic basis underlying trade-off between the two is mostly unknown. Here, we fine-mapped a grain weight QTL using wild emmer introgressions in a durum wheat background and showed that grain weight is associated with the GNI-A1 gene, a ...
Source: TAG. Theoretical and Applied Genetics - May 11, 2019 Category: Genetics & Stem Cells Authors: Golan G, Ayalon I, Perry A, Zimran G, Ade-Ajayi T, Mosquna A, Distelfeld A, Peleg Z Tags: Theor Appl Genet Source Type: research

Haploid male fertility and spontaneous chromosome doubling evaluated in a diallel and recurrent selection experiment in maize.
Abstract KEY MESSAGE: Mainly additive gene action governed inheritance of haploid male fertility, although epistatic effects were also significant. Recurrent selection for haploid male fertility resulted in substantial improvement in this trait. The doubled haploid (DH) technology offers several advantages in maize breeding compared to the traditional method of recurrent selfing. However, there is still great potential for improving the success rate of DH production. Currently, the majority of haploid plants are infertile after chromosome doubling treatment by antimitotic agents such as colchicine and cannot be se...
Source: TAG. Theoretical and Applied Genetics - May 6, 2019 Category: Genetics & Stem Cells Authors: Molenaar WS, Schipprack W, Brauner PC, Melchinger AE Tags: Theor Appl Genet Source Type: research

Genetic architecture of tipburn resistance in lettuce.
re RW Abstract KEY MESSAGE: Two major QTLs for tipburn were identified in LGs 1 and 5 contributing to resistance in cv. Salinas. The findings suggest pleiotropic effects between leaf crinkliness/savoy and tipburn. Tipburn is a physiological disorder in lettuce that is thought to be caused by a localized deficiency of calcium in leaf tissues. To elucidate the genetic architecture of resistance to tipburn in lettuce, seven recombinant inbred line populations were analyzed in multiple environments and years to identify quantitative trait loci (QTLs) for tipburn. Core height, head firmness, head closure, leaf crinklin...
Source: TAG. Theoretical and Applied Genetics - May 4, 2019 Category: Genetics & Stem Cells Authors: Macias-González M, Truco MJ, Bertier LD, Jenni S, Simko I, Hayes RJ, Michelmore RW Tags: Theor Appl Genet Source Type: research

A breeding strategy targeting the secondary gene pool of bread wheat: introgression from a synthetic hexaploid wheat.
Abstract KEY MESSAGE: Introgressing one-eighth of synthetic hexaploid wheat genome through a double top-cross plus a two-phase selection is an effective strategy to develop high-yielding wheat varieties. The continued expansion of the world population and the likely onset of climate change combine to form a major crop breeding challenge. Genetic advances in most crop species to date have largely relied on recombination and reassortment within a relatively narrow gene pool. Here, we demonstrate an efficient wheat breeding strategy for improving yield potentials by introgression of multiple genomic regions of de nov...
Source: TAG. Theoretical and Applied Genetics - May 3, 2019 Category: Genetics & Stem Cells Authors: Hao M, Zhang L, Zhao L, Dai S, Li A, Yang W, Xie D, Li Q, Ning S, Yan Z, Wu B, Lan X, Yuan Z, Huang L, Wang J, Zheng K, Chen W, Yu M, Chen X, Chen M, Wei Y, Zhang H, Kishii M, Hawkesford MJ, Mao L, Zheng Y, Liu D Tags: Theor Appl Genet Source Type: research

A novel high-density grapevine (Vitis vinifera L.) integrated linkage map using GBS in a half-diallel population.
gez A Abstract KEY MESSAGE: A half-diallel population involving five elite grapevine cultivars was generated and genotyped by GBS, and highly-informative segregation data was used to construct a high-density genetic map for Vitis vinifera L. Grapevine is one of the most relevant fruit crops in the world. Deeper genetic knowledge could assist modern grapevine breeding programs to develop new wine grape varieties able to face climate change effects. To assist in the rapid identification of markers for crop yield components, grape quality traits and adaptation potential, we generated a large Vitis vinifera L. populat...
Source: TAG. Theoretical and Applied Genetics - May 3, 2019 Category: Genetics & Stem Cells Authors: Tello J, Roux C, Chouiki H, Laucou V, Sarah G, Weber A, Santoni S, Flutre T, Pons T, This P, Péros JP, Doligez A Tags: Theor Appl Genet Source Type: research

Analysis of recombinant inbred line populations derived from wheat landraces to identify new genes for wheat stem sawfly resistance.
Abstract Wheat landrace accessions were chosen from areas of the world with historical European wheat stem sawfly (Cephus pygmaeus L.) selection pressure to develop six recombinant inbred line (RIL) populations. Molecular maps were constructed, and resistance due to antibiosis and antixenosis was assessed at sites in Montana naturally infested by Cephus cinctus Norton, the wheat stem sawfly (WSS). Novel QTLs were identified along with QTL previously identified in elite germplasm. A newly identified QTL on chromosome 1B provided a new source for pith-filled solid stems. An allele for resistance on chromosome 4A unr...
Source: TAG. Theoretical and Applied Genetics - May 2, 2019 Category: Genetics & Stem Cells Authors: Varella AC, Weaver DK, Blake NK, Hofland ML, Heo HY, Cook JP, Lamb PF, Jordan KW, Akhunov E, Chao S, Talbert LE Tags: Theor Appl Genet Source Type: research

Insights into deployment of DNA markers in plant variety protection and registration.
Abstract KEY MESSAGE: The efficiency of phenotype-based assessments of plant variety protection and registration could be improved by the integration of DNA-based testing. We review the current and proposed models in the era of next-generation breeding. The current plant variety protection system relies on morphological description of plant varieties. Distinctness, uniformity, and stability (DUS) assessments determine whether a new variety is distinguishable from common knowledge varieties and exhibits sufficient phenotypic uniformity and stability during two independent growing cycles. However, DUS assessment can...
Source: TAG. Theoretical and Applied Genetics - May 2, 2019 Category: Genetics & Stem Cells Authors: Jamali SH, Cockram J, Hickey LT Tags: Theor Appl Genet Source Type: research

BjuWRR1, a CC-NB-LRR gene identified in Brassica juncea, confers resistance to white rust caused by Albugo candida.
Abstract KEY MESSAGE: BjuWRR1, a CNL-type R gene, was identified from an east European gene pool line of Brassica juncea and validated for conferring resistance to white rust by genetic transformation. White rust caused by the oomycete pathogen Albugo candida is a significant disease of crucifer crops including Brassica juncea (mustard), a major oilseed crop of the Indian subcontinent. Earlier, a resistance-conferring locus named AcB1-A5.1 was mapped in an east European gene pool line of B. juncea-Donskaja-IV. This line was tested along with some other lines of B. juncea (AABB), B. rapa (AA) and B. nigra (BB) for ...
Source: TAG. Theoretical and Applied Genetics - May 2, 2019 Category: Genetics & Stem Cells Authors: Arora H, Padmaja KL, Paritosh K, Mukhi N, Tewari AK, Mukhopadhyay A, Gupta V, Pradhan AK, Pental D Tags: Theor Appl Genet Source Type: research

Correction to: Genome-wide SNP discovery for development of high-density genetic map and QTL mapping of ascochyta blight resistance in chickpea (Cicer arietinum L.).
Abstract Unfortunately there was an error in the name of the gene "Ca-AKL18" in the discussion section. PMID: 31028410 [PubMed - as supplied by publisher] (Source: TAG. Theoretical and Applied Genetics)
Source: TAG. Theoretical and Applied Genetics - April 27, 2019 Category: Genetics & Stem Cells Authors: Deokar A, Sagi M, Tar'an B Tags: Theor Appl Genet Source Type: research

B-class MADS-box TM6 is a candidate gene for tomato male sterile-1526.
In this study, the ms-1526 locus was fine-mapped to a 44.6 kb interval that contained four putative genes. Thereinto, Solyc02g084630 encodes tomato B-class MADS-box gene TM6 (syn. TDR6), which plays an important role in stamen development. Sequencing revealed that there was a 12.7 kb deletion in the ms-1526 region, where the promoter and first four exons of the TM6 gene were absent. ms-1547, an allele of ms-1526, also contained the same deletion in the TM6 gene. And the other allele ms-15 mutant contained a single-nucleotide polymorphism (SNP, C to A) in the coding region of the TM6 gene, which led to a missense ...
Source: TAG. Theoretical and Applied Genetics - April 24, 2019 Category: Genetics & Stem Cells Authors: Cao X, Liu X, Wang X, Yang M, van Giang T, Wang J, Liu X, Sun S, Wei K, Wang X, Gao J, Du Y, Qin Y, Guo Y, Huang Z Tags: Theor Appl Genet Source Type: research

Genetic mapping of a major QTL promoting homoeologous chromosome pairing in a wheat landrace.
Abstract KEY MESSAGE: Common wheat landrace Kaixian-luohanmai carries a gene(s) that promotes homoeologous chromosome pairing. A major QTL responsible for this effect was mapped to chromosome arm 3AL. Polyhaploid hybrids of a Chinese common wheat landrace Kaixian-luohanmai (KL) and related species show increased levels of chromosome pairing. Over 90% of that pairing is between homoeologous arms of wheat chromosomes, with a very strong preference for pairing between homoeologs from genomes A and D. Wheat-rye pairing was also observed at low frequency. Two mapping populations were created from the hybrids of KL with...
Source: TAG. Theoretical and Applied Genetics - April 23, 2019 Category: Genetics & Stem Cells Authors: Fan C, Luo J, Zhang S, Liu M, Li Q, Li Y, Huang L, Chen X, Ning S, Yuan Z, Zhang L, Wang J, Zheng Y, Liu D, Hao M Tags: Theor Appl Genet Source Type: research

Genome-wide analysis of maize GPAT gene family and cytological characterization and breeding application of ZmMs33/ZmGPAT6 gene.
Abstract KEY MESSAGE: Genome-wide analysis of maize GPAT gene family, cytological characterization of ZmMs33/ZmGPAT6 gene encoding an ER-localized protein with four conserved motifs, and its molecular breeding application in maize. Glycerol-3-phosphate acyltransferase (GPAT) mediates the initial step of glycerolipid biosynthesis and plays pivotal roles in plant growth and development. Compared with GPAT genes in Arabidopsis, our understanding to maize GPAT gene family is very limited. Recently, ZmMs33 gene has been identified to encode a sn-2 GPAT protein and control maize male fertility in our laboratory (Xie et ...
Source: TAG. Theoretical and Applied Genetics - April 23, 2019 Category: Genetics & Stem Cells Authors: Zhu T, Wu S, Zhang D, Li Z, Xie K, An X, Ma B, Hou Q, Dong Z, Tian Y, Li J, Wan X Tags: Theor Appl Genet Source Type: research

A single-base change at a splice site in Wx-A1 caused incorrect RNA splicing and gene inactivation in a wheat EMS mutant line.
Abstract KEY MESSAGE: An EMS-induced single-base mutation at a splice site caused abnormal RNA splicing and resulted in the gene inactivation and the lack of Wx-A1 protein in a wheat EMS mutant line. An EMS-mutagenized population was generated using common wheat cv. SM126 consisting of 10,600 M2 plants. One Wx-A1 null mutant was identified through analyses of 390 grains produced from 130 M2 plants using electrophoresis analyses. The Wx-A1 sequences of parental line SM126 and M2-31 mutant were determined as 2781 bp, and there was only one SNP mutation between them. The SNP was a mutation from G to A at nucleot...
Source: TAG. Theoretical and Applied Genetics - April 16, 2019 Category: Genetics & Stem Cells Authors: Luo M, Ding J, Li Y, Tang H, Qi P, Ma J, Wang J, Chen G, Pu Z, Li W, Li Z, Harwood W, Lan X, Deng M, Lu Z, Wei Y, Zheng Y, Jiang Q Tags: Theor Appl Genet Source Type: research

Testing multiplicative terms in AMMI and GGE models for multienvironment trials with replicates.
Abstract KEY MESSAGE: For analysing multienvironment trials with replicates, a resampling-based method is proposed for testing significance of multiplicative interaction terms in AMMI and GGE models, which is superior compared to contending methods in robustness to heterogeneity of variance. The additive main effects and multiplicative interaction model and genotype main effects and genotype-by-environment interaction model are commonly used for the analysis of multienvironment trial data. Agronomists and plant breeders are frequently using these models for cultivar trials repeated across different environments an...
Source: TAG. Theoretical and Applied Genetics - April 15, 2019 Category: Genetics & Stem Cells Authors: Malik WA, Forkman J, Piepho HP Tags: Theor Appl Genet Source Type: research

Dissection of the genetic variation and candidate genes of lint percentage by a genome-wide association study in upland cotton.
Abstract KEY MESSAGE: A genome-wide associated study identified six novel QTLs for lint percentage. Two candidate genes underlying this trait were also detected. Increasing lint percentage (LP) is a core goal of cotton breeding. To better understand the genetic basis of LP, a genome-wide association study (GWAS) was conducted using 276 upland cotton accessions planted in multiple environments and genotyped with a CottonSNP63K array. After filtering, 10,660 high-quality single-nucleotide polymorphisms (SNPs) were retained. Population structure, principal component and neighbor-joining phylogenetic tree analyses div...
Source: TAG. Theoretical and Applied Genetics - April 13, 2019 Category: Genetics & Stem Cells Authors: Song C, Li W, Pei X, Liu Y, Ren Z, He K, Zhang F, Sun K, Zhou X, Ma X, Yang D Tags: Theor Appl Genet Source Type: research

CRISPR/Cas9-mediated genome editing reveals differences in the contribution of INDEHISCENT homologues to pod shatter resistance in Brassica napus L.
Abstract The INDEHISCENT (IND) and ALCATRAZ (ALC) gene homologues have been reported to be essential for dehiscence of fruits in Brassica species. But their functions for pod shatter resistance in Brassica napus, an important oil crops, are not well understood. Here, we assessed the functions of these two genes in rapeseed using CRISPR/Cas9 technology. The induced mutations were stably transmitted to successive generations, and a variety of homozygous mutants with loss-of-function alleles of the target genes were obtained for phenotyping. The results showed that the function of BnIND gene is essential for pod shat...
Source: TAG. Theoretical and Applied Genetics - April 12, 2019 Category: Genetics & Stem Cells Authors: Zhai Y, Cai S, Hu L, Yang Y, Amoo O, Fan C, Zhou Y Tags: Theor Appl Genet Source Type: research

Fine-mapping of angular leaf spot resistance gene Phg-2 in common bean and development of molecular breeding tools.
Abstract KEY MESSAGE: The Common Bean Angular Leaf Spot Resistance Gene Phg-2 was fine-mapped to a 409-Kbp region, and molecular markers for breeders were developed and validated in field experiments. Common bean (Phaseolus vulgaris L.) is an important food legume in Latin America, Asia and Africa. It is an important source of protein, carbohydrates and micro-minerals, particularly for smallholder farmers. Common bean productivity is affected by angular leaf spot (ALS) disease caused by the pathogenic fungus Pseudocercospora griseola, resulting in significant yield losses, particularly in low-input smallholder far...
Source: TAG. Theoretical and Applied Genetics - April 11, 2019 Category: Genetics & Stem Cells Authors: Gil J, Solarte D, Lobaton JD, Mayor V, Barrera S, Jara C, Beebe S, Raatz B Tags: Theor Appl Genet Source Type: research

Combining pedigree and genomic information to improve prediction quality: an example in sorghum.
Abstract KEY MESSAGE: The use of a kinship matrix integrating pedigree- and marker-based relationships optimized the performance of genomic prediction in sorghum, especially for traits of lower heritability. Selection based on genome-wide markers has become an active breeding strategy in crops. Genomic prediction models can make use of pedigree information to account for the residual polygenic effects not captured by markers. Our aim was to evaluate the impact of using pedigree and genomic information on prediction quality of breeding values for different traits in sorghum. We explored BLUP models that use weighte...
Source: TAG. Theoretical and Applied Genetics - April 9, 2019 Category: Genetics & Stem Cells Authors: Velazco JG, Malosetti M, Hunt CH, Mace ES, Jordan DR, van Eeuwijk FA Tags: Theor Appl Genet Source Type: research

Fine mapping and molecular characterization of the virescent gene vsp in Upland cotton (Gossypium hirsutum).
This study could help us unravel the function of GhPUR4 in chloroplast development and Chl biosynthesis at the early developmental stages of the true leaves in cotton, which could promote the research and application of virescent mutations in cotton heterosis breeding. PMID: 30953093 [PubMed - as supplied by publisher] (Source: TAG. Theoretical and Applied Genetics)
Source: TAG. Theoretical and Applied Genetics - April 5, 2019 Category: Genetics & Stem Cells Authors: Mao G, Wei H, Hu W, Ma Q, Zhang M, Wang H, Yu S Tags: Theor Appl Genet Source Type: research

Fine-mapping of the Fusarium head blight resistance QTL Qfhs.ifa-5A identifies two resistance QTL associated with anther extrusion.
Abstract KEY MESSAGE: Fine-mapping separated Qfhs.ifa-5A into a major QTL mapping across the centromere and a minor effect QTL positioned at the distal half of 5AS. Both increase Fusarium resistance and anther extrusion. The Fusarium head blight (FHB) resistance QTL Qfhs.ifa-5A resides in the low-recombinogenic pericentromeric region of chromosome 5A making fine-mapping particularly arduous. Qfhs.ifa-5A primarily contributes resistance to fungal entry with the favorable allele descending from the highly Fusarium resistant cultivar Sumai-3. Fine-mapping a near-isogenic recombinant inbred line population partitioned...
Source: TAG. Theoretical and Applied Genetics - April 4, 2019 Category: Genetics & Stem Cells Authors: Steiner B, Buerstmayr M, Wagner C, Danler A, Eshonkulov B, Ehn M, Buerstmayr H Tags: Theor Appl Genet Source Type: research

Drought and heat stress-related proteins: an update about their functional relevance in imparting stress tolerance in agricultural crops.
We describe here the recent developments about the involvement of diverse stress-related proteins in sensing, signaling, and defending the cells in plants in response to drought or/and heat stress. In the current era of global climate drift, plant growth and productivity are often limited by various environmental stresses, especially drought and heat. Adaptation to abiotic stress is a multigenic process involving maintenance of homeostasis for proper survival under adverse environment. It has been widely observed that a series of proteins respond to heat and drought conditions at both transcriptional and translational leve...
Source: TAG. Theoretical and Applied Genetics - April 2, 2019 Category: Genetics & Stem Cells Authors: Priya M, Dhanker OP, Siddique KHM, HanumanthaRao B, Nair RM, Pandey S, Singh S, Varshney RK, Prasad PVV, Nayyar H Tags: Theor Appl Genet Source Type: research

Fine mapping and identification of the fuzzless gene GaFzl in DPL972 (Gossypium arboreum).
Abstract KEY MESSAGE: The fuzzless gene GaFzl was fine mapped to a 70-kb region containing a GIR1 gene, Cotton_A_11941, responsible for the fuzzless trait in Gossypium arboreum DPL972. Cotton fiber is the most important natural textile resource. The fuzzless mutant DPL972 (Gossypium arboreum) provides a useful germplasm resource to explore the molecular mechanism underlying fiber and fuzz initiation and development. In our previous research, the fuzzless gene in DPL972 was identified as a single dominant gene and named GaFzl. In the present study, we fine mapped this gene using F2 and BC1 populations. By combining...
Source: TAG. Theoretical and Applied Genetics - April 2, 2019 Category: Genetics & Stem Cells Authors: Feng X, Cheng H, Zuo D, Zhang Y, Wang Q, Liu K, Ashraf J, Yang Q, Li S, Chen X, Song G Tags: Theor Appl Genet Source Type: research

Genome-wide mapping of adult plant stripe rust resistance in wheat cultivar Toni.
Abstract KEY MESSAGE: Two adult plant stripe rust resistance QTL, QYrto.swust-3AS and QYrto.swust-3BS, were identified and mapped in common wheat cultivar Toni. The two QTL were located to corresponding positions in the wheat physical map position based on flanking SNP markers. Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is one of the most important foliar diseases of wheat. Characterization and utilization of resistance genes are the most effective, economic and environmental-friendly way to control the disease. The wheat cultivar Toni resistant at the adult plant stage to predominant Chines...
Source: TAG. Theoretical and Applied Genetics - April 2, 2019 Category: Genetics & Stem Cells Authors: Zhou X, Hu T, Li X, Yu M, Li Y, Yang S, Huang K, Han D, Kang Z Tags: Theor Appl Genet Source Type: research

CLAVATA signaling pathway genes modulating flowering time and flower number in chickpea.
Abstract KEY MESSAGE: A combinatorial genomic strategy delineated functionally relevant natural allele of a CLAVATA gene and its marker (haplotype)-assisted introgression led to development of the early-flowering chickpea cultivars with high flower number and enhanced yield/productivity. Unraveling the genetic components involved in CLAVATA (CLV) signaling is crucial for modulating important shoot apical meristem (SAM) characteristics and ultimately regulating diverse SAM-regulated agromorphological traits in crop plants. A genome-wide scan identified 142 CLV1-, 28 CLV2- and 6 CLV3-like genes, and their comprehens...
Source: TAG. Theoretical and Applied Genetics - March 30, 2019 Category: Genetics & Stem Cells Authors: Basu U, Narnoliya L, Srivastava R, Sharma A, Bajaj D, Daware A, Thakro V, Malik N, Upadhyaya HD, Tripathi S, Hegde VS, Tyagi AK, Parida SK Tags: Theor Appl Genet Source Type: research

Introgression of the chromosomal region with the Pi-cd locus from Oryza meridionalis into O. sativa L. during rice domestication.
Abstract KEY MESSAGE: The genotype of the Pi-cd locus found in blast-resistant rice variety Kitakurin, which is a cultivated rice from Japan belonging to Oryza sativa japonica, is identical to that of its wild relative O. meridionalis. Crop domestication from wild relatives to cultivated species has encompassed significant phenotypic changes. However, little is known about the genetic changes involved in domestication. Here, we surveyed the origin of the Pi-cd locus across Oryza species with AA genomes by comparison with the genome sequences of Hoshinoyume (HS), which does not carry the Pi-cd blast resistance gene...
Source: TAG. Theoretical and Applied Genetics - March 26, 2019 Category: Genetics & Stem Cells Authors: Fujino K, Hirayama Y, Obara M, Ikegaya T Tags: Theor Appl Genet Source Type: research

Dissection of two quantitative trait loci with pleiotropic effects on plant height and spike length linked in coupling phase on the short arm of chromosome 2D of common wheat (Triticum aestivum L.).
Abstract KEY MESSAGE: Two QTL with pleiotropic effects on plant height and spike length linked in coupling phase on chromosome 2DS were dissected, and diagnostic marker for each QTL was developed. Plant height (PHT) is a crucial trait related to plant architecture and yield potential, and dissection of its underlying genetic basis would help to improve the efficiency of designed breeding in wheat. Here, two quantitative trait loci (QTL) linked in coupling phase on the short arm of chromosome 2D with pleiotropic effects on PHT and spike length, QPht/Sl.cau-2D.1 and QPht/Sl.cau-2D.2, were separated and characterized...
Source: TAG. Theoretical and Applied Genetics - March 26, 2019 Category: Genetics & Stem Cells Authors: Chai L, Chen Z, Bian R, Zhai H, Cheng X, Peng H, Yao Y, Hu Z, Xin M, Guo W, Sun Q, Zhao A, Ni Z Tags: Theor Appl Genet Source Type: research

Effects of Rht-B1 and Ppd-D1 loci on pollinator traits in wheat.
Abstract KEY MESSAGE: Elite wheat pollinators are critical for successful hybrid breeding. We identified Rht-B1 and Ppd-D1 loci affecting multiple pollinator traits and therefore represent major targets for improving hybrid seed production. Hybrid breeding has a great potential to significantly boost wheat yields. Ideal male pollinators would be taller in stature, contain many spikelets well-spaced along the spike and exhibit high extrusion of large anthers. Most importantly, flowering time would match with that of the female parent. Available genetic resources for developing an elite wheat pollinator are limited,...
Source: TAG. Theoretical and Applied Genetics - March 21, 2019 Category: Genetics & Stem Cells Authors: Okada T, Jayasinghe JEARM, Eckermann P, Watson-Haigh NS, Warner P, Hendrikse Y, Baes M, Tucker EJ, Laga H, Kato K, Albertsen M, Wolters P, Fleury D, Baumann U, Whitford R Tags: Theor Appl Genet Source Type: research

Mapping of barley susceptibility/resistance QTL against spot form net blotch caused by Pyrenophora teres f. maculata using RIL populations.
Abstract Spot form net blotch (SFNB) caused by the necrotrophic fungal pathogen Pyrenophora teres f. maculata (Ptm) is an important disease of barley worldwide including the major barley production regions of North America. To characterize SFNB resistance/susceptibility quantitative trait loci (QTL), three recombinant inbred line (RIL) populations were developed from crosses between the malting barley cultivars, Tradition (six row) and Pinnacle (two row), and the two world barley core collection lines, PI67381 and PI84314. Tradition and Pinnacle were susceptible to many North American Ptm isolates, while PI67381 a...
Source: TAG. Theoretical and Applied Genetics - March 20, 2019 Category: Genetics & Stem Cells Authors: Tamang P, Richards JK, Alhashal A, Sharma Poudel R, Horsley RD, Friesen TL, Brueggeman RS Tags: Theor Appl Genet Source Type: research

QTL mapping for maize starch content and candidate gene prediction combined with co-expression network analysis.
Abstract KEY MESSAGE: A major QTL Qsta9.1 was identified on chromosome 9, combined with GWAS, and co-expression network analysis showed that GRMZM2G110929 and GRMZM5G852704 are the potential candidates for association with maize kernel starch content. Increasing maize kernel starch content may not only lead to higher maize kernel yields and qualities, but also help meet industry demands. By using the intermated B73 × Mo17 population, QTLs were mapped for starch content in this study. A major QTL Qsta9.1 was detected in a 1.7 Mb interval on chromosome 9 and validated by allele frequency ana...
Source: TAG. Theoretical and Applied Genetics - March 19, 2019 Category: Genetics & Stem Cells Authors: Lin F, Zhou L, He B, Zhang X, Dai H, Qian Y, Ruan L, Zhao H Tags: Theor Appl Genet Source Type: research

Assessment of the effect of ten heading time genes on reproductive transition and yield components in rice using a CRISPR/Cas9 system.
In this study, we generated 14 heading time mutants using CRISPR/Cas9 gene-editing technology and marker-assisted selection with a japonica Sasanishiki wild-type (WT) genetic background. Photoperiod sensitivity, the relationship between days to heading (DTH), and yield components of mutants were investigated. We found that the yield increases with increases in DTH, but eventually plateaus at maximum and then began to decrease, whereas the biomass continued to increase. The mutants exerted distinctly different effects on DTH and yield components. The convergent double mutants had severe yield reduction compared with single ...
Source: TAG. Theoretical and Applied Genetics - March 19, 2019 Category: Genetics & Stem Cells Authors: Cui Y, Zhu M, Xu Z, Xu Q Tags: Theor Appl Genet Source Type: research

Technological perspectives for plant breeding.
PMID: 30888430 [PubMed - as supplied by publisher] (Source: TAG. Theoretical and Applied Genetics)
Source: TAG. Theoretical and Applied Genetics - March 19, 2019 Category: Genetics & Stem Cells Authors: Godwin ID, Rutkoski J, Varshney RK, Hickey LT Tags: Theor Appl Genet Source Type: research

The effects of training population design on genomic prediction accuracy in wheat.
Abstract Genomic selection offers several routes for increasing the genetic gain or efficiency of plant breeding programmes. In various species of livestock, there is empirical evidence of increased rates of genetic gain from the use of genomic selection to target different aspects of the breeder's equation. Accurate predictions of genomic breeding value are central to this, and the design of training sets is in turn central to achieving sufficient levels of accuracy. In summary, small numbers of close relatives and very large numbers of distant relatives are expected to enable predictions with higher accuracy. To...
Source: TAG. Theoretical and Applied Genetics - March 19, 2019 Category: Genetics & Stem Cells Authors: Edwards SM, Buntjer JB, Jackson R, Bentley AR, Lage J, Byrne E, Burt C, Jack P, Berry S, Flatman E, Poupard B, Smith S, Hayes C, Gaynor RC, Gorjanc G, Howell P, Ober E, Mackay IJ, Hickey JM Tags: Theor Appl Genet Source Type: research

Evaluation of the genetic architecture and the potential of genomics-assisted breeding of quality traits in two large panels of durum wheat.
In this study, we evaluated the quality traits protein content, sedimentation volume, falling number, vitreousity and thousand kernel weight in a Central European (CP) and a Southern and Western European panel (SP) with 183 and 159 durum lines, respectively, and investigated their genetic architecture by genome-wide association mapping. Except for protein content, we identified QTL explaining a large proportion of the genotypic variance for different traits. However, most of them were identified only in one panel. Nevertheless, for sedimentation volume a genomic region on chromosome 1B appeared important in both durum pane...
Source: TAG. Theoretical and Applied Genetics - March 18, 2019 Category: Genetics & Stem Cells Authors: Rapp M, Sieber A, Kazman E, Leiser WL, Würschum T, Longin CFH Tags: Theor Appl Genet Source Type: research

Genome-wide SNP discovery for development of high-density genetic map and QTL mapping of ascochyta blight resistance in chickpea (Cicer arietinum L.).
The objective of this study was to identify genetic loci and candidate genes controlling the resistance to ascochyta blight in recombinant inbred lines derived from crossing cultivars Amit and ICCV 96029. The RILs were genotyped using the genotyping-by-sequencing procedure and Illumina® GoldenGate array. The RILs were evaluated in the field over three site-years and in three independent greenhouse experiments. A genetic map with eight linkage groups was constructed using 3430 SNPs. Eight QTLs for resistance were identified on chromosomes 2, 3, 4, 5 and 6. The QTLs individually explained 7-40% of the phenotypic variatio...
Source: TAG. Theoretical and Applied Genetics - March 16, 2019 Category: Genetics & Stem Cells Authors: Deokar A, Sagi M, Tar'an B Tags: Theor Appl Genet Source Type: research

Testcross performance of doubled haploid lines from European flint maize landraces is promising for broadening the genetic base of elite germplasm.
AE Abstract KEY MESSAGE: Selected doubled haploid lines averaged similar testcross performance as their original landraces, and the best of them approached the yields of elite inbreds, demonstrating their potential to broaden the narrow genetic diversity of the flint germplasm pool. Maize landraces represent a rich source of genetic diversity that remains largely idle because the high genetic load and performance gap to elite germplasm hamper their use in modern breeding programs. Production of doubled haploid (DH) lines can mitigate problems associated with the use of landraces in pre-breeding. Our objective was...
Source: TAG. Theoretical and Applied Genetics - March 15, 2019 Category: Genetics & Stem Cells Authors: Brauner PC, Schipprack W, Utz HF, Bauer E, Mayer M, Schön CC, Melchinger AE Tags: Theor Appl Genet Source Type: research

Genetic diversity and parentage analysis of grape rootstocks.
In this report, we developed nuclear and chloroplast SSR fingerprint data from rootstock selections maintained in germplasm collections, compared them to develop a reference dataset, and carried out parentage analysis to resolve previously reported, and determine new, breeding records. We refined and updated the parentage of 26 rootstocks based on 21 nuclear and 14 chloroplast markers. Results indicate that 39% of the genetic background of analyzed rootstocks originated from only three accessions of three grape species: Vitis berlandieri cv. Rességuier 2, V. rupestris cv. du Lot and V. riparia cv. Gloire de Montpell...
Source: TAG. Theoretical and Applied Genetics - March 8, 2019 Category: Genetics & Stem Cells Authors: Riaz S, Pap D, Uretsky J, Laucou V, Boursiquot JM, Kocsis L, Andrew Walker M Tags: Theor Appl Genet Source Type: research

Stable and novel QTL identification and new insights into the genetic networks affecting seed fiber traits in Brassica napus.
In this study, the genetic basis of seed fiber biosynthesis in B. napus was investigated via quantitative trait locus (QTL) analysis using a doubled haploid population derived from 'KenC-8' crossed with 'N53-2.' Seed lignin content (LC), cellulose content (CC) and hemicellulose content (HC) were significantly negatively correlated with seed oil content (OC). Co-localization QTLs among LC, CC, HC and OC on A09 were found with contributions ranging from 9.87 to 48.50%. Seven co-localization QTLs involved in the fiber component and OC were further verified by bulked segregant analysis (BSA). The unique QTL uqA9-12 might ...
Source: TAG. Theoretical and Applied Genetics - March 4, 2019 Category: Genetics & Stem Cells Authors: Miao L, Chao H, Chen L, Wang H, Zhao W, Li B, Zhang L, Li H, Wang B, Li M Tags: Theor Appl Genet Source Type: research

Genetic mapping of powdery mildew resistance genes in soybean by high-throughput genome-wide sequencing.
In this study, resistance to M. diffusa among resistant varieties B3, Fudou234, and B13 is mapped as a single Mendelian locus using three mapping populations derived from crossing susceptible with resistant cultivars. The position of the PMD resistance locus in B3 is located between simple sequence repeat (SSR) markers GMES6959 and Satt_393 on chromosome 16, at genetic distances of 7.1 cM and 4.6 cM, respectively. To more finely map the PMD resistance gene, a high-density genetic map was constructed using 248 F8 recombinant inbred lines derived from a cross of Guizao1 × B13. The final map incl...
Source: TAG. Theoretical and Applied Genetics - March 2, 2019 Category: Genetics & Stem Cells Authors: Jiang B, Li M, Cheng Y, Cai Z, Ma Q, Jiang Z, Ma R, Xia Q, Zhang G, Nian H Tags: Theor Appl Genet Source Type: research

Enhancing the rate of genetic gain in public-sector plant breeding programs: lessons from the breeder's equation.
Abstract KEY MESSAGE: The integration of new technologies into public plant breeding programs can make a powerful step change in agricultural productivity when aligned with principles of quantitative and Mendelian genetics. The breeder's equation is the foundational application of quantitative genetics to crop improvement. Guided by the variables that describe response to selection, emerging breeding technologies can make a powerful step change in the effectiveness of public breeding programs. The most promising innovations for increasing the rate of genetic gain without greatly increasing program size appear to b...
Source: TAG. Theoretical and Applied Genetics - March 1, 2019 Category: Genetics & Stem Cells Authors: Cobb JN, Juma RU, Biswas PS, Arbelaez JD, Rutkoski J, Atlin G, Hagen T, Quinn M, Ng EH Tags: Theor Appl Genet Source Type: research

Molecular characterization of a novel TaGL3-5A allele and its association with grain length in wheat (Triticum aestivum L.).
Abstract KEY MESSAGE: We isolated a novel allele associated with grain length and grain weight in wheat, TaGL3-5A-G. The TaGL3-5A-G allele frequency is low in wheat, so it has potential for breeding. Selection of large-grain wheat showing big grain sink potential and strong sink activity is becoming an important objective in breeding programs. Here, we cloned a wheat TaGL3-5A gene that was orthologous to rice GL3 and was phylogenetically clustered with both monocot PPKL1 and its expression pattern was similar to grain size change at early and middle stages of seed development. The isolated TaGL3-5A genomic sequenc...
Source: TAG. Theoretical and Applied Genetics - March 1, 2019 Category: Genetics & Stem Cells Authors: Yang J, Zhou Y, Wu Q, Chen Y, Zhang P, Zhang Y, Hu W, Wang X, Zhao H, Dong L, Han J, Liu Z, Cao T Tags: Theor Appl Genet Source Type: research

HL2 on chromosome 7D of wheat (Triticum aestivum L.) regulates both head length and spikelet number.
Abstract KEY MESSAGE: A major QTL QSpl.nau-7D, named HL2, was validated for its effects on head length and kernel number per spike using NIL, and mapped to a 0.2 cM interval using recombinants. Improvement in wheat inflorescence traits such as spike or head length and spikelet number provides an important avenue to increase grain yield potential. In a previous study, QSpl.nau-7D, the major QTL for head length on chromosome 7D, was identified in the recombinant inbred lines derived from Nanda2419 and Wangshuibai. To validate and precisely map this QTL, the Wangshuibai allele was transferred to elite cultivar Y...
Source: TAG. Theoretical and Applied Genetics - February 27, 2019 Category: Genetics & Stem Cells Authors: Yao H, Xie Q, Xue S, Luo J, Lu J, Kong Z, Wang Y, Zhai W, Lu N, Wei R, Yang Y, Han Y, Zhang Y, Jia H, Ma Z Tags: Theor Appl Genet Source Type: research

Simultaneous selection for grain yield and protein content in genomics-assisted wheat breeding.
tmayr H Abstract KEY MESSAGE: Large genetic improvement can be achieved by simultaneous genomic selection for grain yield and protein content when combining different breeding strategies in the form of selection indices. Genomic selection has been implemented in many national and international breeding programmes in recent years. Numerous studies have shown the potential of this new breeding tool; few have, however, taken the simultaneous selection for multiple traits into account that is though common practice in breeding programmes. The simultaneous improvement in grain yield and protein content is thereby a maj...
Source: TAG. Theoretical and Applied Genetics - February 27, 2019 Category: Genetics & Stem Cells Authors: Michel S, Löschenberger F, Ametz C, Pachler B, Sparry E, Bürstmayr H Tags: Theor Appl Genet Source Type: research

Bulked segregant RNA-sequencing (BSR-seq) identified a novel rare allele of eIF4E effective against multiple isolates of BaYMV/BaMMV.
ng P Abstract KEY MESSAGE: A novel rare allele of the barley host factor gene eIF4E for BaMMV/BaYMV infection was identified in an Iranian landrace that showed broad resistance to barley yellow mosaic virus disease, and molecular markers facilitating efficient selection were developed. The soil-borne yellow mosaic virus disease caused by different strains of barley yellow mosaic virus (BaYMV) and barley mild mosaic virus (BaMMV) is a major threat to winter barley (Hordeum vulgare) production in Europe and East Asia. However, the exploration of resistant germplasm or casual genes for barley breeding is rather limit...
Source: TAG. Theoretical and Applied Genetics - February 27, 2019 Category: Genetics & Stem Cells Authors: Shi L, Jiang C, He Q, Habekuß A, Ordon F, Luan H, Shen H, Liu J, Feng Z, Zhang J, Yang P Tags: Theor Appl Genet Source Type: research

Genome-wide association study of seed protein, oil and amino acid contents in soybean from maturity groups I to IV.
Abstract KEY MESSAGE: Genomic regions associated with seed protein, oil and amino acid contents were identified by genome-wide association analyses. Geographic distributions of haplotypes indicate scope of improvement of these traits. Soybean [Glycine max (L.) Merr.] protein and oil are used worldwide in feed, food and industrial materials. Increasing seed protein and oil contents is important; however, protein content is generally negatively correlated with oil content. We conducted a genome-wide association study using phenotypic data collected from five environments for 621 accessions in maturity groups I-IV an...
Source: TAG. Theoretical and Applied Genetics - February 26, 2019 Category: Genetics & Stem Cells Authors: Lee S, Van K, Sung M, Nelson R, LaMantia J, McHale LK, Mian MAR Tags: Theor Appl Genet Source Type: research

Technological advances in maize breeding: past, present and future.
t T Abstract Maize has for many decades been both one of the most important crops worldwide and one of the primary genetic model organisms. More recently, maize breeding has been impacted by rapid technological advances in sequencing and genotyping technology, transformation including genome editing, doubled haploid technology, parallelled by progress in data sciences and the development of novel breeding approaches utilizing genomic information. Herein, we report on past, current and future developments relevant for maize breeding with regard to (1) genome analysis, (2) germplasm diversity characterization and ut...
Source: TAG. Theoretical and Applied Genetics - February 23, 2019 Category: Genetics & Stem Cells Authors: Andorf C, Beavis WD, Hufford M, Smith S, Suza WP, Wang K, Woodhouse M, Yu J, Lübberstedt T Tags: Theor Appl Genet Source Type: research

QTL analysis of durable stripe rust resistance in the North American winter wheat cultivar Skiles.
This study determined the effects of growth stage and temperature on expression of high-temperature adult-plant resistance to stripe rust, mapped six QTL for durable resistance in winter wheat Skiles using a doubled haploid population, and selected breeding lines with different combinations of the QTL using marker-assisted selection. The winter wheat cultivar Skiles has a high level of high-temperature adult-plant (HTAP) resistance to stripe rust caused by Puccinia striiformis f. sp. tritici (Pst). The Skiles HTAP resistance was highly effective at the adult-plant stage even under low temperatures, but high temperatures in...
Source: TAG. Theoretical and Applied Genetics - February 22, 2019 Category: Genetics & Stem Cells Authors: Liu L, Yuan CY, Wang MN, See DR, Zemetra RS, Chen XM Tags: Theor Appl Genet Source Type: research